A spokeswoman for British Prime Minister Theresa May said Johnson did not reflect the government's position on Saudi Arabia when he made his remarks a a week ago during a conference in Rome
Speaking during a panel discussion, Johnson blamed a lack of strong leadership for division in the region, saying, "You've got the Saudis, Iran, everybody, moving in, and puppeteering and playing proxy wars, and it's a tragedy to watch it."
The comments, first reported by Britain's Guardian newspaper, ran counter to Britain's longstanding support for Saudi Arabia, a key ally in the Middle East.
They were particularly sensitive since they emerged in the wake of a visit by May to the region.
"Those are the Foreign Secretary's views. They are not the government's position on Saudi and its role in the region," Prime Minister Theresa May's spokeswoman said during a regular media briefing Thursday.
"The Foreign Secretary will be in the region this weekend. He will be in Saudi Arabia on Sunday and will have the opportunity to set out the way the UK sees its relationship with Saudi and the work we want to do with them and other partners to bring an end to the appalling conflict in Yemen," the spokeswoman added.
Asked if Johnson was expected to apologize to Saudi leaders on Sunday, May's spokeswoman said: "He will have meetings with senior representatives sin Saudi Arabia and he will have the opportunity to set out the government's position."
Johnson, who was appointed foreign secretary by May in July, is known for his outspoken ways and sometimes less than diplomatic use of language
May's spokeswoman declined to confirm whether the pair had talked since Johnson's comments about Saudi Arabia became public. "The Prime Minister has full confidence in the Foreign Secretary," she added.
Johnson: Politicians 'twisting and abusing religion'
Speaking at the Mediterranean Dialogues in Rome on December 1, Johnson said leaders in the Middle East were not willing to reach out beyond their own Sunni, Shia or other religious group to "bring people together and to develop a national story again."
He also suggested they were using religion for political ends.
"There are politicians who are twisting and abusing religion and different strains of the same religion in order to further their own political objectives," he said. "That's one of the biggest political problems in the whole region.
"And the tragedy for me -- and that's why you have these proxy wars being fought the whole time in that area -- is that there is not strong enough leadership in the countries themselves."
CNN has reached out to Saudi Arabia but it has not yet responded to a request for comment.
An Iranian Foreign Ministry source told CNN that Iran is currently studying the comments made by Johnson and will react to them soon.
May promises Gulf defense spending
In a speech Wednesday to the Gulf Cooperation Council Summit in Bahrain, May promised £3 billion (about $3.78 billion) in defense spending in the region over the next decade.
She also hailed Britain's longstanding friendships with members of the Gulf Cooperation Council, which brings together Saudi Arabia, Kuwait, the United Arab Emirates, Qatar, Oman and Bahrain.
May, who was the first woman to address the Gulf Cooperation Council summit, has been under pressure at home to stop arms sales to Saudi Arabia over its role in the war in neighboring Yemen
While Saudi Arabia leads a coalition aimed at restoring the internationally recognized Yemeni government to power, Iran -- a major regional Shia power -- backs the rebel Houthi movement, which has seized the capital, Sanaa.
Taking a populist line
CNN Diplomatic Editor Nic Robertson writes: Johnson is oversimplifying and overstating, taking a populist line at a time when it has become popular to bash the Saudi government.
There is no doubt that Saudi Arabia and Iran are engaged in proxy wars in Yemen and Syria, but it's hard to accuse these countries of having weak leadership. As to the question of religion, the Sunni-Shia divide is fundamental in these wars.
It's a bad message for the British Prime Minister at the wrong time. Undoubtedly the Saudis will complain through back channels to the British.
When May first appointed Johnson Foreign Secretary, on her first full day in office, many thought the often outspoken politician wouldn't last.
These comments in Rome, surfacing just as May was concluding big business deals in the Middle East -- including with Saudi Arabia -- may be seen as his worst transgression so far.
Only days ago, German Foreign Minister Frank-Walter Steinmeier said -- during a joint press conference with the Foreign Secretary -- that he was "not particularly amused" that Johnson backed Brexit.
As Britain's chief overseas diplomat, his comments have the potential to inflame situations and anger politicians. And he seems to be expanding his ability to create waves from Europe into the Middle East.